Hi Sergej,
"--write-index" is a valid option for samtools view in 1.10 (provided your data
is sorted). My question, more clearly, would be "can you specify csi index for
bam output instead of bai"?
Regards,
Keiran Raine, M.Sc., MBCS
Principal Software Developer
Cancer, Ageing and Somatic Mutation
Wellcome Sanger Institute
k...@sanger.ac.uk<mailto:k...@sanger.ac.uk>
Office: D3-19
Ext: 4983
Please note that due to childcare requirements during the Covid lockdown I am
generally not available after 4pm.
From: "Nowoshilow,Sergej" <sergej.nowoshi...@imp.ac.at>
Date: Saturday, 13 June 2020 at 19:30
To: Keiran Raine <k...@sanger.ac.uk>, "samtools-help@lists.sourceforge.net"
<samtools-help@lists.sourceforge.net>
Subject: Re: [Samtools-help] --write-index - csi? [EXT]
Hi Keiran,
I don’t think so. As far as I know, samtools view is only used to convert (or
view) SAM<->BAM<->CRAM. However, the file must not be sorted, while indexing
implies that the file is sorted.
I’d use ‘samtools view’ to convert the file if necessary, sort it using
‘samtools sort’ and then ‘samtools index -c’ to index the resulting file.
Best,
Sergej
Dr. Sergej Nowoshilow
Post-doc in Tanaka Lab
Elly Tanaka group, IMP
Animal models of regeneration
email: sergej.nowoshi...@imp.ac.at
phone: +43 (0) 1 79730 3203
orcid: 0000-0001-8360-5010
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Von: Keiran Raine <k...@sanger.ac.uk>
Datum: Samstag, 13. Juni 2020 um 20:16
An: "samtools-help@lists.sourceforge.net" <samtools-help@lists.sourceforge.net>
Betreff: [Samtools-help] --write-index - csi?
Hi,
Is it possible to write a csi index when using samtools view? I can't see
anything in the --output-fmt* section relating to index format.
Thanks,
Keiran Raine, M.Sc., MBCS
Principal Software Developer
Cancer, Ageing and Somatic Mutation
Wellcome Sanger Institute
k...@sanger.ac.uk<mailto:k...@sanger.ac.uk>
Office: D3-19
Ext: 4983
Please note that due to childcare requirements during the Covid lockdown I am
generally not available after 4pm.
-- The Wellcome Sanger Institute is operated by Genome Research Limited, a
charity registered in England with number 1021457 and a company registered in
England with number 2742969, whose registered office is 215 Euston Road,
London, NW1 2BE.
--
The Wellcome Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
company registered in England with number 2742969, whose registered
office is 215 Euston Road, London, NW1 2BE.
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